Multi-axis imaging systems such as array microscopes, in which a plurality of optical elements are movable in unison and arranged in an array so as to image respective portions of a common object, have been discussed in, for example, U.S. Pat. Nos. 6,842,290; 6,958,464; 7,061,584; 7,482,566; and 7,864,369. As the topography of an object (such as a surface) being imaged does not necessarily fall within the depth of focus range of the array of objectives Multiple objective are concurrently translated along an optical axis to simultaneously image different portions of the object. However, when topography of the object is such that some portions of the object being imaged are not within the depth of focus of the corresponding objective, at least some of the images produced by the array microscope are blurred. Since topography of a given object is often unpredictable and may erratically deviate from an imaged surface on which the objectives are focused, there is a need for system and method for correction of deviations of object topography to conform to the imaged surface.